A conceptual model for translating omic data into clinical action by Timothy M Herr, Suzette J Bielinski, Erwin Bottinger, Ariel Brautbar, Murray Brilliant, Christopher G Chute, Joshua Denny, Robert R Freimuth, Andrea Hartzler, Joseph Kannry, Isaac S Kohane, Iftikhar J Kullo, Simon Lin, Jyotishman Pathak, Peggy Peissig, Jill Pulley, James Ralston, Luke Rasmussen, Dan Roden, Gerard Tromp, Marc S Williams, Justin Starren

“…Genomic, proteomic, epigenomic, and other "omic" data have the potential to enable precision medicine, also commonly referred to as personalized medicine. …”
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Novel insights into histone lysine methyltransferases in cancer therapy: From epigenetic regulation to selective drugs by Qili Liao, Jie Yang, Shengfang Ge, Peiwei Chai, Jiayan Fan, Renbing Jia

“…The reversible and precise temporal and spatial regulation of histone lysine methyltransferases (KMTs) is essential for epigenome homeostasis. The dysregulation of KMTs is associated with tumor initiation, metastasis, chemoresistance, invasiveness, and the immune microenvironment. …”
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Hallmarks of Aging in the Liver by Nicholas J. Hunt, Sun Woo (Sophie) Kang, Glen P. Lockwood, David G. Le Couteur, Victoria C. Cogger

“…The aging process in the liver is driven by alterations of the genome and epigenome that contribute to dysregulation of mitochondrial function and nutrient sensing pathways, leading to cellular senescence and low-grade inflammation. …”
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Elucidating distinct molecular signatures of Lewy body dementias by Joshua Harvey, Ehsan Pishva, Leonidas Chouliaras, Katie Lunnon

“…However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. …”
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Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines by Aaron L. Statham, Phillippa C. Taberlay, Theresa K. Kelly, Peter A. Jones, Susan J. Clark

“…During carcinogenesis, the expression of many genes is altered alongside extensive changes in the epigenome, with repressed genes often being associated with local DNA hypermethylation and gain of nucleosomes at their promoters. …”
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DNA methylation aging clocks: challenges and recommendations by Christopher G. Bell, Robert Lowe, Peter D. Adams, Andrea A. Baccarelli, Stephan Beck, Jordana T. Bell, Brock C. Christensen, Vadim N. Gladyshev, Bastiaan T. Heijmans, Steve Horvath, Trey Ideker, Jean-Pierre J. Issa, Karl T. Kelsey, Riccardo E. Marioni, Wolf Reik, Caroline L. Relton, Leonard C. Schalkwyk, Andrew E. Teschendorff, Wolfgang Wagner, Kang Zhang, Vardhman K. Rakyan

“…This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. …”
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The Evolving Landscape of Male Varicocele Pathophysiology in the Era of Multi-Omics: A Narrative Review of the Current Literature by Carlos Munoz-Lopez, Anne Wong, Kieran Lewis, Raevti Bole, Sarah C. Vij, Scott D. Lundy

“…Specifically, we review the literature describing the underlying causes of varicoceles, discuss the molecular and cellular mechanisms causing pathological changes in some (but not all) men, and highlight key articles regarding the next-generation analyses (e.g., transcriptome, epigenome, proteome, and microbiome) being applied to better understand the condition and its treatment. …”
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ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C by Yousra Ben Zouari, Anne M. Molitor, Natalia Sikorska, Vera Pancaldi, Tom Sexton

“…The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.…”
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shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R [v2; ref status: indexed, http://f1000r.es/4e3] by Jean-Philippe Fortin, Elana Fertig, Kasper Hansen

“…Altogether, the package makes it easy to perform quality assessment of large-scale methylation datasets, such as epigenome-wide association studies or the datasets available through The Cancer Genome Atlas portal. …”
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Monitoring and quantifying replication fork dynamics with high-throughput methods by Nora Fajri, Nataliya Petryk

“…These technologies have illuminated the regulation of genome replication programs, quantified the impact of DNA replication on genomic mutations and evolutionary processes, and elucidated the mechanisms of replication-coupled chromatin assembly and epigenome maintenance.…”
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sciMET-cap: high-throughput single-cell methylation analysis with a reduced sequencing burden by Sonia N. Acharya, Ruth V. Nichols, Lauren E. Rylaarsdam, Brendan L. O’Connell, Theodore P. Braun, Andrew C. Adey

“…Abstract DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. …”
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Cancer Biology, Epidemiology, and Treatment in the 21st Century: Current Status and Future Challenges From a Biomedical Perspective by Patricia Piña-Sánchez PhD, Antonieta Chávez-González PhD, Martha Ruiz-Tachiquín PhD, Eduardo Vadillo PhD, Alberto Monroy-García PhD, Juan José Montesinos PhD, Rocío Grajales MD, Marcos Gutiérrez de la Barrera MD, PhD, Hector Mayani PhD

“…Today, we understand cancer at the genomic and epigenomic levels, and we have identified the cell that starts neoplastic transformation and characterized the mechanisms for the invasion of other tissues. …”
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Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR by Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian

“…However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). …”
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Blossom of CRISPR technologies and applications in disease treatment by Huayi Liu, Lian Wang, Yunzi Luo

“…In addition to genome editing, CRISPR has been developed as a variety of tools for gene expression regulations, live cell chromatin imaging, base editing, epigenome editing, and nucleic acid detection. Moreover, in the context of further boosting the usability and feasibility of CRISPR systems, novel CRISPR systems and engineered CRISPR protein mutants have been explored and studied actively. …”
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First person – Claudia Figueroa-Romero and Benjamin Murdock

“…Claudia Figueroa-Romero and Benjamin Murdock are co-first authors on ‘ Temporal evolution of the microbiome, immune system and epigenome with disease progression in ALS mice’, published in DMM. …”
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One-carbon metabolism and ionizing radiation: a multifaceted interaction by Miousse Isabelle R., Tobacyk Julia, Melnyk Stepan, James S. Jill, Cheema Amrita K., Boerma Marjan, Hauer-Jensen Martin, Koturbash Igor

“…In this conceptual review, we propose the IR-induced changes to one-carbon metabolism as prerequisites to alterations in the cellular epigenome. We also provide evidence from both experimental and clinical studies describing the interactions between IR and one-carbon metabolism. …”
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Circling back to epigenetic regulation in osteosarcoma: Comment on ‘Hsa_circ_0088212-mediated miR-520h/APOA1 axis inhibits the osteosarcoma progression’ by ‘ Hao Peng’ by Kaniz Fatema, Jared J. Barrott

“…Osteosarcoma is a genetically complex cancer, thus there are increasing efforts to identify biomarkers and regulators within the epigenome that can better predict patient outcomes and provide new therapeutic targets. …”
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Multi-CUT&Tag to simultaneously profile multiple chromatin factors by Sneha Gopalan, Thomas G. Fazzio

“…Although slightly more laborious than CUT&Tag, multi-CUT&Tag provides a powerful option for generating multi-factor maps for epigenomic profiling.For complete details on the use and execution of this protocol, please refer to Gopalan et al. (2021).…”
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Genome-wide studies in prostate cancer poised liquid biopsy as a molecular discovery tool by Nicholas Lo, Housheng Hansen He, Housheng Hansen He, Sujun Chen, Sujun Chen

“…Recent genome-wide liquid biopsy studies in prostate cancer analyzing plasma samples have provided insights into the genome and epigenome dynamics during disease progression. In-depth genomic sequencing can offer a comprehensive understanding of cancer evolution, enabling more accurate clinical decision-making. …”
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Epigenetic reprogramming in cancer: From diagnosis to treatment by Pedro Mikael da Silva Costa, Pedro Mikael da Silva Costa, Sarah Leyenne Alves Sales, Sarah Leyenne Alves Sales, Daniel Pascoalino Pinheiro, Larissa Queiroz Pontes, Larissa Queiroz Pontes, Sarah Sant’Anna Maranhão, Claudia do Ó. Pessoa, Claudia do Ó. Pessoa, Claudia do Ó. Pessoa, Gilvan Pessoa Furtado, Gilvan Pessoa Furtado, Cristiana Libardi Miranda Furtado, Cristiana Libardi Miranda Furtado

“…Given the reversible nature of epigenetic modifications, the ability to restore the cancer epigenome through the inhibition of the epigenetic modifiers is a promising therapy for cancer treatment, either as a monotherapy or in combination with other anticancer therapies, including immunotherapies. …”
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